scholarly journals Replicative transposition contributes to the evolution and dissemination of KPC-2-producing plasmid in Enterobacterales

2021 ◽  
pp. 1-124
Author(s):  
Yu Tang ◽  
Gang Li ◽  
Pinghua Shen ◽  
Ying Zhang ◽  
Xiaofei Jiang
Keyword(s):  
Replicative Transposition

DNA inversion mediated by the r-determinant of plasmid NR1: Evidence for the intramolecular replicative transposition of a 23 kb IS1-flanked transposon?

1986 ◽  
Vol 205 (3) ◽  
pp. 572-574 ◽  
Author(s):  
Shigeru Iida ◽  
Christine Hänni ◽  
Jürg Meyer ◽  
Werner Arber
Keyword(s):  
Dna Inversion ◽  
Replicative Transposition

Participation of hup gene product in replicative transposition of Mu phage in Escherichia coli

Gene ◽  
1989 ◽  
Vol 76 (2) ◽  
pp. 353-358 ◽  
Author(s):  
Yasunobu Kano ◽  
Naoki Goshima ◽  
Morimasa Wada ◽  
Fumio Imamoto
Keyword(s):  
Escherichia Coli ◽  
Gene Product ◽  
Replicative Transposition

scholarly journals Helraiser intermediates provide insight into the mechanism of eukaryotic replicative transposition

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Ivana Grabundzija ◽  
Alison B. Hickman ◽  
Fred Dyda
Keyword(s):  
Replicative Transposition ◽  
Insight Into

scholarly journals IS26-Mediated Precise Excision of the IS26-aphA1a Translocatable Unit

mBio ◽  
2015 ◽  
Vol 6 (6) ◽  
Author(s):  
Christopher J. Harmer ◽  
Ruth M. Hall
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
High Frequency ◽  
Antibiotic Resistance Genes ◽  
Kanamycin Resistance ◽  
Gram Negative Bacteria ◽  
Critical Determinant ◽  
Gram Negative ◽  
Precise Excision ◽  
Replicative Transposition

ABSTRACTWe recently showed that, in the absence of RecA-dependent homologous recombination, the Tnp26 transposase catalyzes cointegrate formation via a conservative reaction between two preexisting IS26, and this is strongly preferred over replicative transposition to a new site. Here, the reverse reaction was investigated by assaying for precise excision of the central region together with a single IS26from a compound transposon bounded by IS26. In arecAmutant strain, Tn4352, a kanamycin resistance transposon carrying theaphA1agene, was stable. However, loss of kanamycin resistance due to precise excision of the translocatable unit (TU) from the closely related Tn4352B, leaving behind the second IS26, occurred at high frequency. Excision occurred when Tn4352B was in either a high- or low-copy-number plasmid. The excised circular segment, known as a TU, was detected by PCR. Excision required the IS26transposase Tnp26. However, the Tnp26 of only one IS26in Tn4352B was required, specifically the IS26downstream of theaphA1agene, and the excised TU included the active IS26. The frequency of Tn4352B TU loss was influenced by the context of the transposon, but the critical determinant of high-frequency excision was the presence of three G residues in Tn4352B replacing a single G in Tn4352.These G residues are located immediately adjacent to the two G residues at the left end of the IS26that is upstream of theaphA1agene. Transcription oftnp26was not affected by the additional G residues, which appear to enhance Tnp26 cleavage at this end.IMPORTANCEResistance to antibiotics limits treatment options. In Gram-negative bacteria, IS26plays a major role in the acquisition and dissemination of antibiotic resistance. IS257(IS431) and IS1216, which belong to the same insertion sequence (IS) family, mobilize resistance genes in staphylococci and enterococci, respectively. Many different resistance genes are found in compound transposons bounded by IS26, and multiply and extensively antibiotic-resistant Gram-negative bacteria often include regions containing several antibiotic resistance genes and multiple copies of IS26. We recently showed that in addition to replicative transposition, IS26can use a conservative movement mechanism in which an incoming IS26targets a preexisting one, and this reaction can create these regions. This mechanism differs from that of all the ISs examined in detail thus far. Here, we have continued to extend understanding of the reactions carried out by IS26by examining whether the reverse precise excision reaction is also catalyzed by the IS26transposase.

scholarly journals Rates of transposition in Escherichia coli

2013 ◽  
Vol 9 (6) ◽  
pp. 20130838 ◽  
Author(s):  
Ana Sousa ◽  
Catarina Bourgard ◽  
Lindi M. Wahl ◽  
Isabel Gordo
Keyword(s):  
Escherichia Coli ◽  
Transposable Elements ◽  
Selective Pressure ◽  
Previous Knowledge ◽  
E Coli ◽  
Transposition Rate ◽  
Replicative Transposition ◽  
Evolutionary Role ◽  
Excision Rate

The evolutionary role of transposable elements (TEs) is still highly controversial. Two key parameters, the transposition rate ( u and w , for replicative and non-replicative transposition) and the excision rate ( e ) are fundamental to understanding their evolution and maintenance in populations. We have estimated u , w and e for six families of TEs (including eight members: IS1, IS2, IS3, IS4, IS5, IS30, IS150 and IS186) in Escherichia coli , using a mutation accumulation (MA) experiment. In this experiment, mutations accumulate essentially at the rate at which they appear, during a period of 80 500 (1610 generations × 50 lines) generations, and spontaneous transposition events can be detected. This differs from other experiments in which insertions accumulated under strong selective pressure or over a limited genomic target. We therefore provide new estimates for the spontaneous rates of transposition and excision in E. coli . We observed 25 transposition and three excision events in 50 MA lines, leading to overall rate estimates of u ∼ 1.15 × 10 –5 , w ∼ 4 × 10 −8 and e ∼ 1.08 × 10 −6 (per element, per generation). Furthermore, extensive variation between elements was found, consistent with previous knowledge of the mechanisms and regulation of transposition for the different elements.

Use of retrotransposon-derived genetic markers to analyse genomic variability in plants

2019 ◽  
Vol 46 (1) ◽  
pp. 15 ◽  
Author(s):  
Ruslan Kalendar ◽  
Asset Amenov ◽  
Asset Daniyarov
Keyword(s):  
Genetic Diversity ◽  
Digital Pcr ◽  
Genomic Variability ◽  
Plant Genomes ◽  
Anchored Pcr ◽  
Copy And Paste ◽  
Somatic Transposition ◽  
Replicative Transposition ◽  
Eukaryotic Genomes ◽  
Generation Sequencing

Transposable elements (TEs) are common mobile genetic elements comprising several classes and making up the majority of eukaryotic genomes. The movement and accumulation of TEs has been a major force shaping the genes and genomes of most organisms. Most eukaryotic genomes are dominated by retrotransposons and minimal DNA transposon accumulation. The ‘copy and paste’ lifecycle of replicative transposition produces new genome insertions without excising the original element. Horizontal TE transfer among lineages is rare. TEs represent a reservoir of potential genomic instability and RNA-level toxicity. Many TEs appear static and nonfunctional, but some are capable of replicating and mobilising to new positions, and somatic transposition events have been observed. The overall structure of retrotransposons and the domains responsible for the phases of their replication are highly conserved in all eukaryotes. TEs are important drivers of species diversity and exhibit great variety in their structure, size and transposition mechanisms, making them important putative actors in evolution. Because TEs are abundant in plant genomes, various applications have been developed to exploit polymorphisms in TE insertion patterns, including conventional or anchored PCR, and quantitative or digital PCR with primers for the 5ʹ or 3ʹ junction. Alternatively, the retrotransposon junction can be mapped using high-throughput next-generation sequencing and bioinformatics. With these applications, TE insertions can be rapidly, easily and accurately identified, or new TE insertions can be found. This review provides an overview of the TE-based applications developed for plant species and assesses the contributions of TEs to the analysis of plants’ genetic diversity.

scholarly journals Replacement of the Bacteriophage Mu Strong Gyrase Site and Effect on Mu DNA Replication

1999 ◽  
Vol 181 (18) ◽  
pp. 5783-5789 ◽  
Author(s):  
M. L. Pato ◽  
M. Banerjee
Keyword(s):  
Escherichia Coli ◽  
Dna Replication ◽  
Bacteriophage Mu ◽  
Chromosomal Dna ◽  
E Coli ◽  
Repeat Sequences ◽  
Central Fragment ◽  
Entire Chromosome ◽  
Nucleoid Structure ◽  
Replicative Transposition

ABSTRACT The bacteriophage Mu strong gyrase site (SGS) is required for efficient replicative transposition and functions by promoting the synapsis of prophage termini. To look for other sites which could substitute for the SGS in promoting Mu replication, we have replaced the SGS in the middle of the Mu genome with fragments of DNA from various sources. A central fragment from the transposing virus D108 allowed efficient Mu replication and was shown to contain a strong gyrase site. However, neither the strong gyrase site from the plasmid pSC101 nor the major gyrase site from pBR322 could promote efficient Mu replication, even though the pSC101 site is a stronger gyrase site than the Mu SGS as assayed by cleavage in the presence of gyrase and the quinolone enoxacin. To look for SGS-like sites in the Escherichia coli chromosome which might be involved in organizing nucleoid structure, fragments of E. coli chromosomal DNA were substituted for the SGS: first, repeat sequences associated with gyrase binding (bacterial interspersed mosaic elements), and, second, random fragments of the entire chromosome. No fragments were found that could replace the SGS in promoting efficient Mu replication. These results demonstrate that the gyrase sites from the transposing phages possess unusual properties and emphasize the need to determine the basis of these properties.

scholarly journals Transposable elements in natural populations of Drosophila melanogaster

2010 ◽  
Vol 365 (1544) ◽  
pp. 1219-1228 ◽  
Author(s):  
Yuh Chwen G. Lee ◽  
Charles H. Langley
Keyword(s):  
Transposable Elements ◽  
Dna Sequences ◽  
Copy Number ◽  
Population Genomics ◽  
Natural Populations ◽  
Crossing Over ◽  
Large Role ◽  
Essential Components ◽  
Replicative Transposition

Transposable elements (TEs) are families of small DNA sequences found in the genomes of virtually all organisms. The sequences typically encode essential components for the replicative transposition sequences of that TE family. Thus, TEs are simply genomic parasites that inflict detrimental mutations on the fitness of their hosts. Several models have been proposed for the containment of TE copy number in outbreeding host populations such as Drosophila . Surveys of the TEs in genomes from natural populations of Drosophila have played a central role in the investigation of TE dynamics. The early surveys indicated that a typical TE insertion is rare in a population, which has been interpreted as evidence that each TE is selected against. The proposed mechanisms of this natural selection are reviewed here. Subsequent and more targeted surveys identify heterogeneity among types of TEs and also highlight the large role of homologous and possibly ectopic crossing over in the dynamics of the Drosophila TEs. The recent discovery of germline-specific RNA interference via the piwi-interacting RNA pathway opens yet another interesting mechanism that may be critical in containing the copy number of TEs in natural populations of Drosophila . The expected flood of Drosophila population genomics is expected to rapidly advance understanding of the dynamics of TEs.

scholarly journals Mutants of Escherichia coli defective for replicative transposition of bacteriophage Mu.

1986 ◽  
Vol 167 (3) ◽  
pp. 905-919 ◽  
Author(s):  
W Ross ◽  
S H Shore ◽  
M M Howe
Keyword(s):  
Escherichia Coli ◽  
Bacteriophage Mu ◽  
Replicative Transposition

scholarly journals The Left End of IS2: a Compromise between Transpositional Activity and an Essential Promoter Function That Regulates the Transposition Pathway

2004 ◽  
Vol 186 (3) ◽  
pp. 858-865 ◽  
Author(s):  
Leslie A. Lewis ◽  
Edruge Cylin ◽  
Ho Kyung Lee ◽  
Robert Saby ◽  
Wilson Wong ◽  
...  
Keyword(s):  
Second Step ◽  
Inverted Repeats ◽  
Sequence Information ◽  
Linear Element ◽  
Strong Promoter ◽  
Transpositional Activity ◽  
Hybrid Promoter ◽  
Optimal Function ◽  
Replicative Transposition ◽  
Novel Variation

ABSTRACT Cut-and-paste (simple insertion) and replicative transposition pathways are the two classical paradigms by which transposable elements are mobilized. A novel variation of cut and paste, a two-step transposition cycle, has recently been proposed for insertion sequences of the IS3 family. In IS2 this variation involves the formation of a circular, putative transposition intermediate (the minicircle) in the first step. Two aspects of the minicircle may involve its proposed role in the second step (integration into the target). The first is the presence of a highly reactive junction formed by the two abutted ends of the element. The second is the assembly at the minicircle junction of a strong hybrid promoter which generates higher levels of transposase. In this report we show that IS2 possesses a highly reactive minicircle junction at which a strong promoter is assembled and that the promoter is needed for the efficient completion of the pathway. We show that the sequence diversions which characterize the imperfect inverted repeats or ends of this element have evolved specifically to permit the formation and optimal function of this promoter. While these sequence diversions eliminate catalytic activity of the left end (IRL) in the linear element, sufficient sequence information essential for catalysis is retained by the IRL in the context of the minicircle junction. These data confirm that the minicircle is an essential intermediate in the two-step transposition pathway of IS2.

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